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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 55 records · Page 3
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Matrix-formation dynamics dictate methyl nitrite conformer abundance

Methyl nitrite has two stable conformational isomers resulting from rotation about the primary C–O–N–O dihedral angle: cis-CH 3 ONO and trans-CH 3 ONO, with cis being more stable by ∼5 kJ/mol. Here, the barrier to rotational interconversion (∼45 kJ/mol) is too large for isomerization to occur under ambient conditions. This paper presents evidence of a change in conformer abundance when dilute CH 3 ONO is deposited onto a cold substrate; the relative population of the freshly deposited cis conformer is seen to increase compared to its gas-phase abundance, measured by in situ infrared spectroscopy. We observe abundance changes depending on the identity of the bath gas (N 2 , Ar, and Xe) and deposition angle. The observations indicate that the surface properties of the growing matrix influence conformer abundance—contrary to the widely held assumption that conformer abundance in matrices reflects gas-phase abundance. We posit that differences in the angle-dependent host-gas deposition dynamics affect the growing surfaces, causing changes in conformer abundances. Quantum chemistry calculations of the binding energies between CH 3 ONO and a single bath-gas component reveal that significant energetic stabilization is not observed in 1:1 complexes of N 2 :CH 3 ONO, Ar:CH 3 ONO, or Xe:CH 3 ONO. From our results, we conclude that the growing surface plays a significant role in trapping cis-CH 3 ONO more effectively than trans-CH 3 ONO, likely because cis-CH 3 ONO is more compact. Taken together, the observations highlight the necessity for careful characterization of conformers in matrix-isolated systems, emphasizing a need for further study into the deposition dynamics and surface structure of chemically inert matrices.

Hockey, Emily K.↗
DOE OSTI2024

Scale and conformal invariance on (A)dS spacetimes

We examine the question of scale versus conformal invariance on maximally symmetric curved backgrounds and study general two-derivative conformally invariant free theories of vectors and tensors. For spacetime dimension D > 4 , these conformal theories can be diagonalized into standard massive fields in which unbroken conformal symmetry nontrivially mixes components of different spins. In D = 4 , the tensor case becomes a conformal theory mixing a partially massless spin-2 field with a massless spin-1 field. For massless linearized gravity in D = 4 , we confirm through direct calculation that correlation functions of gauge-invariant operators take the conformally invariant form, despite the absence of standard conformal symmetry at the level of the action. Published by the American Physical Society 2024

Astronomy & Astrophysics↗
DOE OSTI2022

Optimizing conformance control for gas injection EOR in unconventional reservoirs

Field observations have shown that interference between wells caused by connected fractures commonly exists in unconventional reservoirs. The well interference effect and conformance issues could lead to minimal enhanced oil recovery response (EOR) in actual operations if they are not properly controlled. A series of data analysis, modeling, and experimental activities were performed in this study to investigate the gas EOR strategies in the Bakken Formation. Employing the embedded discrete fracture modeling technology, a multiple-well, multiple-fracture model was developed to capture the well interference and conformance issues in the Bakken. The model made it possible to investigate the complex flow behavior between wells in the EOR (huff ‘n’ puff) processes. Alternative EOR and conformance control strategies using water and surfactant injections were studied to improve oil production performance based on experimental observations. Results showed that water injection could be used for conformance control in the Bakken because of its relatively low mobility compared to gas; however, water could also block oil flow around the conformance control wells because of the high interfacial tension between oil and water. Adding surfactant to the injection water is more effective for improving gas EOR performance since surfactant reduces the oil–water interfacial tension and contact angle effectively. Up to 9.4% more oil could be produced from the huff ‘n’ puff wells in 2 years of EOR operations when rich gas was injected at only 3 MMscf/d with 6000 psi of surfactant injection in the offset wells for conformance control.

42 ENGINEERING↗
DOE OSTI2024

Data-Efficient Generation of Protein Conformational Ensembles with Backbone-to-Side-Chain Transformers

Excitement at the prospect of using data-driven generative models to sample configurational ensembles of biomolecular systems stems from the extraordinary success of these models on a diverse set of high-dimensional sampling tasks. Unlike image generation or even the closely related problem of protein structure prediction, there are currently no data sources with sufficient breadth to parametrize generative models for conformational ensembles. To enable discovery, a fundamentally different approach to building generative models is required: models should be able to propose rare, albeit physical, conformations that may not arise in even the largest data sets. Here, in this work, we introduce a modular strategy to generate conformations based on “backmapping” from a fixed protein backbone that (1) maintains conformational diversity of the side chains and (2) couples the side-chain fluctuations using global information about the protein conformation. Our model combines simple statistical models of side-chain conformations based on rotamer libraries with the now ubiquitous transformer architecture to sample with atomistic accuracy. Together, these ingredients provide a strategy for rapid data acquisition and hence a crucial ingredient for scalable physical simulation with generative neural networks.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Uncovering Backbone Conformation for Rigid DPP-Based Donor–Acceptor Conjugated Polymer Using Deuterium Labeling and Neutron Scattering

The conjugated polymer’s backbone conformation dictates the delocalization of electrons, ultimately affecting its optoelectronic properties. Most conjugated polymers can be viewed as semirigid rods with their backbone embedded among long alkyl side chains. Thus, it is challenging to experimentally quantify the conformation of a conjugated backbone. Here, we performed contrast variation neutron scattering on rigid conjugated donor–acceptor (D–A) diketopyrrolopyrrole (DPP) polymers with selectively deuterated side chains to measure the conjugated backbone conformation. We first synthesized DPPbased polymers with deuterated side chains, confirmed by NMR and FTIR. Using contrast variation neutron scattering, we found that the DPP-based conjugated polymers are much more rigid than poly(3-alkylthiophenes), with persistence length (L p ) at 16–18 nm versus 2–3 nm. More importantly, in contrast to the relatively flexible poly(3-alkylthiophenes) whose backbone is more flexible than the whole polymer, we found that the backbone of DPP-based polymers has the same L p value compared to the whole polymer chain. This indicates that side chain interference on backbone conformation is not present for the semirigid polymer, which is further confirmed by coarse-grained molecular dynamics (CG-MD) simulations. Our work provides a novel protocol to probe polymer’s backbone conformation and paradigm-shifting understanding of the backbone conformation of semirigid conjugated polymers.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Bootstrapping smooth conformal defects in Chern-Simons-matter theories

Abstract The expectation value of a smooth conformal line defect in a CFT is a conformal invariant functional of its path in space-time. For example, in largeNholographic theories, these fundamental observables are dual to the open-string partition function in AdS. In this paper, we develop a bootstrap method for studying them and apply it to conformal line defects in Chern-Simons matter theories. In these cases, the line bootstrap is based on three minimal assumptions — conformal invariance of the line defect, largeNfactorization, and the spectrum of the two lowest-lying operators at the end of the line. On the basis of these assumptions, we solve the one-dimensional CFT on the line and systematically compute the defect expectation value in an expansion around the straight line. We find that the conformal symmetry of a straight defect is insufficient to fix the answer. Instead, imposing the conformal symmetry of the defect along an arbitrary curved line leads to a functional bootstrap constraint. The solution to this constraint is found to be unique.

Physics↗
DOE OSTI2021

Cauchy data space and multisymplectic formulation of conformal classical field theories

In this article we inspect the dynamics of classical field theories with a local conformal behavior. Our interest in the multisymplectic setting comes from its suitable description of field theories, and the conformal character has been added to account for field theories that are scale invariant, flat spaces, and because some conformal fields can be exactly solved or classified. In particular, we will solve the example of a conformal scalar field using the geometric Hamilton–Jacobi theory that is explicitly proposed for conformal fields on a multisymplectic manifold. To complete the geometric approach to study field theories, we propose the Hamilton–Jacobi theory for conformal fields in a Cauchy data space, in which space and time are split separately and the dynamics is depicted in an infinite-dimensional manifold.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2026

Noncanonical folding of peptoid oligomers: Formation of a closed conformation in nonpolar solvent

Peptoids provide a versatile platform for foldamer design, yet their conformational behavior in low-dielectric media remains poorly understood. The structural characteristics of N-1-phenylethylglycine (Nspe) homo-oligomers were inves-tigated in chloroform, a solvent that mimics the interior of lipid bilayers, using nuclear magnetic resonance (NMR) spec-troscopy and molecular dynamics (MD) simulations. Nspe7 populated two distinct compact conformations, while Nspe10 adopted a single homogeneous conformation related to the previously reported Nspe9 threaded-loop structure. Integrated experimental and computational analysis reveals that these structures are stabilized by cooperative end-to-end intramo-lecular hydrogen bonding, cis-trans backbone isomerism, and hydrophobic side-chain shielding. The resulting structures minimize exposed polar surface area, demonstrating a closed conformation in the low-dielectric environment. These find-ings establish specific chain-length requirements for achieving well-defined closed conformations. This work provides insights into peptoid folding in nonpolar media, enabling rational design strategies for solvent-directed conformational switching systems.

Oh, Jinyoung↗
DOE OSTI2025

Ligand efficacy shifts a nuclear receptor conformational ensemble between transcriptionally active and repressive states

Abstract Nuclear receptors (NRs) are thought to dynamically alternate between transcriptionally active and repressive conformations, which are stabilized upon ligand binding. Most NR ligand series exhibit limited bias, primarily consisting of transcriptionally active agonists or neutral antagonists, but not repressive inverse agonists—a limitation that restricts understanding of the functional NR conformational ensemble. Here, we report a NR ligand series for peroxisome proliferator-activated receptor gamma (PPARγ) that spans a pharmacological spectrum from repression (inverse agonism) to activation (agonism) where subtle structural modifications switch compound activity. While crystal structures provide snapshots of the fully repressive state, NMR spectroscopy and conformation-activity relationship analysis reveals that compounds within the series shift the PPARγ conformational ensemble between transcriptionally active and repressive conformations that are natively populated in the apo/ligand-free ensemble. Our findings reveal a molecular framework for minimal chemical modifications that enhance PPARγ inverse agonism and elucidate their influence on the dynamic PPARγ conformational ensemble.

Science & Technology - Other Topics↗
DOE OSTI2026

A curated benchmark for cofolding models on kinase conformational states

Abstract Protein kinases are critical drug targets, requiring therapeutics that can modulate their active and inactive conformational states. While cofolding models can generate global folds directly from kinase sequences and ligand SMILES strings, these models have not yet been tested on their ability to recover ligand-induced-fit conformational states of the kinase proteins. Here, we introduce KinConfBench, a curated benchmark of 2225 high-quality human kinase chains to evaluate the ability of four state-of-the-art cofolding models—Boltz-2, Chai-1, Protenix, and RoseTTAFold-All-Atom—to recover both canonical and rare conformational states. We show that geometric success metrics of a ligand pose in the active site do not correlate strongly with the correct kinase conformational state, motivating a new set of dynamical benchmarks for assessing cofolding models. While all four cofolding models achieve ~60–80% prediction accuracy for kinase conformational classification, they exhibit severe mode collapse when performing multiple inferences, show negligible structural diversity in sampling induced-fit motions, and display a prevalent “apo-drift” in which most cofolding models predominantly predict the kinase to be in its ligand-free state. Our results highlight that capturing ligand-induced protein conformational diversity, not just geometric fit, is critical for next-generation structure-based drug discovery.

Sun, Kunyang↗
DOE OSTI2020

Trapping conformational states of a flavin-dependent N-monooxygenase in crystallo reveals protein and flavin dynamics

The siderophore biosynthetic enzyme A (SidA) ornithine hydroxylase from Aspergillus fumigatus is a fungal disease drug target involved in the production of hydroxamate-containing siderophores, which are used by the pathogen to sequester iron. SidA is an N -monooxygenase that catalyzes the NADPH-dependent hydroxylation of l -ornithine through a multistep oxidative mechanism, utilizing a C4a-hydroperoxyflavin intermediate. Here we present four new crystal structures of SidA in various redox and ligation states, including the first structure of oxidized SidA without NADP(H) or l -ornithine bound (resting state). The resting state structure reveals a new out active site conformation characterized by large rotations of the FAD isoalloxazine around the C1–'C2' and N10–C1' bonds, coupled to a 10-Å movement of the Tyr-loop. Additional structures show that either flavin reduction or the binding of NADP(H) is sufficient to drive the FAD to the in conformation. The structures also reveal protein conformational changes associated with the binding of NADP(H) and l -ornithine. Some of these residues were probed using site-directed mutagenesis. Docking was used to explore the active site of the out conformation. These calculations identified two potential ligand-binding sites. Altogether, our results provide new information about conformational dynamics in flavin-dependent monooxygenases. Overall, understanding the different active site conformations that appear during the catalytic cycle may allow fine-tuning of inhibitor discovery efforts.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Conformal geometry from entanglement

In a physical system with conformal symmetry, observables depend on cross-ratios, measures of distance invariant under global conformal transformations (conformal geometry for short). We identify a quantum information-theoretic mechanism by which the conformal geometry emerges at the gapless edge of a 2+1D quantum many-body system with a bulk energy gap. We introduce a novel pair of information-theoretic quantities (\mathfrak{c}_{\textrm{tot}}, \eta) ( 𝔠 tot , η ) that can be defined locally on the edge from the wavefunction of the many-body system, without prior knowledge of any distance measure. We posit that, for a topological groundstate, the quantity \mathfrak{c}_{\textrm{tot}} 𝔠 tot is stationary under arbitrary variations of the quantum state, and study the logical consequences. We show that stationarity, modulo an entanglement-based assumption about the bulk, implies (i) \mathfrak{c}_{\textrm{tot}} 𝔠 tot is a non-negative constant that can be interpreted as the total central charge of the edge theory. (ii) \eta η is a cross-ratio, obeying the full set of mathematical consistency rules, which further indicates the existence of a distance measure of the edge with global conformal invariance. Thus, the conformal geometry emerges from a simple assumption on groundstate entanglement. We show that stationarity of \mathfrak{c}_{\textrm{tot}} 𝔠 tot is equivalent to a vector fixed-point equation involving \eta η , making our assumption locally checkable. We also derive similar results for 1+1D systems under a suitable set of assumptions.

Kim, Isaac H.↗
DOE OSTI2026

Continuous Family of Conformal Field Theories and Exactly Marginal Operators

Does a conformal manifold imply the existence of exactly marginal operators? We answer this question affirmatively under the assumption that there exists a conformal interface with certain properties connecting nearby conformal field theories. We show that the exactly marginal operator that connects the conformal field theories can be reconstructed from the interface displacement operator. Our construction is model independent and based on the general principles of conformal symmetry.

conformal field theory↗
DOE OSTI2020

Dynamics of Cation-Induced Conformational Changes in Nanometer-Sized Uranyl Peroxide Clusters

Conformational changes of the pyrophosphate (Pp)-functionalized uranyl peroxide nanocluster [(UO 2 ) 24 (O 2 ) 24 (P 2 O 7 ) 12 ] 48– ({U 24 Pp 12 }), dissolved as a Li/Na salt, can be induced by the titration of alkali cations into solution. The most symmetric conformer of the molecule has idealized octahedral ( O h ) molecular symmetry. One-dimensional 31 P NMR experiments provide direct evidence that both K + and Rb + ions trigger an O h -to- D 4 h conformational change within {U 24 Pp 12 }. Variable-temperature 31 P NMR experiments conducted on partially titrated {U 24 Pp 12 } systems show an effect on the rates; increased activation enthalpy and entropy for the D 4 h -to- O h transition is observed in the presence of Rb + compared to K + . Two-dimensional, exchange spectroscopy 31 P NMR revealed that magnetization transfer links chemically unique Pp bridges that are present in the D 4 h conformation and that this magnetization transfer occurs via a conformational rearrangement mechanism as the bridges interconvert between two symmetries. The interconversion is triggered by the departure and reentry of K (or Rb) cations out of and into the cavity of the cluster. This rearrangement allows Pp bridges to interconvert without the need to break bonds. Cs ions exhibit unique interactions with {U 24 Pp 12 } clusters and cause only minor changes in the solution 31 P NMR signatures, suggesting that O h symmetry is conserved. Single-crystal X-ray diffraction measurements reveal that the mixed Li/Na/Cs salt adopts D 2 h molecular symmetry, implying that while solvated, this cluster is in equilibrium with a more symmetric form. Thus, these results highlight the unusually flexible nature of the actinide-based {U 24 Pp 12 } and its sensitivity to countercations in solution.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Polymer Conformations and Diffusion Through a Monolayer of Confining Nanoparticles

We present coarse-grained molecular dynamics simulations to probe chain-scale polymer conformations and diffusion between confining nanoparticles (NPs). By constructing a monolayer of hexagonally-packed NPs in a polymer melt with athermal interactions, we observe the magnitude and length-scale over which homogeneously confining NPs impact the polymer behavior, which provides fundamental insights into more complex polymer nanocomposites. We show that polymer conformations are more perturbed under strong confinement (i.e. when the interparticle distance, ID, is less than twice the polymer radius of gyration, 2R g ) as compared to around an isolated NP, and the effect depends on the ratio of R NP /R g rather than either independently. In fact, these conformations can be quantitatively replicated by executing a simple random walk in a similarly confining environment. We also show that polymer diffusion is slowed by the presence of NPs and the slowing persists far beyond the length-scale over which polymer conformations are perturbed. Although the slowing is strongest ~R g from the NPs, the diffusion coefficient is slower even beyond ~5R g from the NPs. Furthermore, by analyzing the directional van Hove distributions, we show polymer diffusion away from the NP monolayer is bulk-like while diffusion through the monolayer is slower with increasing NP confinement. Furthermore, these molecular dynamics simulations provide fundamental insights into the temporal and spatial effect of confining, athermal NPs on chain-scale polymer conformations and diffusion.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Chain Conformations of TEMPO-Based Organic Radical Polymers with Varying Radical Loading and Temperature in Battery-Relevant Solvents

Poly(2,2,6,6-tetramethylpiperidinyloxy-4-yl methacrylate) (PTMA) is an organic radical polymer that is a promising active material in organic batteries. The proximity of the radical groups impacts the nature of charge transfer, in which closer packing promotes electron exchange; however, the chain conformation of PTMA is not well understood. Here, the conformation of PTMA in, and its thermodynamic interactions with, battery-relevant solvents is determined using small-angle neutron scattering (SANS). N-methyl-2-pyrrolidone (NMP) and 50:50 (wt %) ethylene carbonate/dimethyl carbonate (EC/DMC) mixtures with PTMA of varying radical content (68 vs 98%) and temperature (25 and 60 °C) are examined. Both solvents are theta solvents for PTMA irrespective of radical loading and temperature. PTMA attains an expanded chain conformation in NMP and a more compact polymer chain conformation in EC/DMC. Lastly, the electrochemical performance of PTMA films formed from EC/DMC shows improved performance relative to those cast from NMP, which is interpreted to indicate that the compact conformation of PTMA in EC/DMC enables improved inter- and intrachain charge transfer.

25 ENERGY STORAGE↗
DOE OSTI2025

Resonant Tender X-ray Scattering for Disclosing the Backbone Conformation of Conjugated Polymers

The backbone conformation of conjugated polymers (CPs) is essential to their performance in electronic applications. Contrast-variation small-angle neutron scattering (CV-SANS) techniques were used to assess the CP’s backbone conformation, which relies on synthesis of deuterated polymers. Such a technique has been proven mature and effective. One drawback is that deuteration labeling might subtly alter polymer’s physical properties due to structural modifications. To address these challenges, we introduce a novel approach utilizing tender Xray scattering near the sulfur K-edge to distinctly evaluate the backbone versus whole chain conformation for a low-bandgap donor−acceptor CP, poly[(5,6-difluoro- 2,1,3-benzothiadiazol-4,7-diyl)-alt-(3,3‴-dialkyl-2,2′;5′,2″;5″,2‴-quaterthiophen-5,5‴- diyl)] (PffBT4T). For PffBT4T dissolved in trimethylbenzene (TMB), the sulfur K-edge is identified at approximately 2477 eV using near-edge X-ray absorption fine structure spectroscopy (NEXAFS). Tender X-ray scattering conducted at presulfur K-edge and on-sulfur K-edge at elevated temperatures facilitated the distinction between the backbone and whole chain conformations. The results demonstrate that for highly flexible polymer, the backbone’s persistence length could be lower than that of the whole chains, suggesting a more flexible backbone. This rapid, label-free method enhances our ability to characterize CP’s backbone conformation efficiently, offering significant implications for the design and optimization of CPs for advanced electronics.

36 MATERIALS SCIENCE↗
DOE OSTI2025

From sequence to protein structure and conformational dynamics with artificial intelligence/machine learning

The 2024 Nobel Prize in Chemistry was awarded in part for de novo protein structure prediction using AlphaFold2, an artificial intelligence/machine learning (AI/ML) model trained on vast amounts of sequence and three-dimensional structure data. AlphaFold2 and related models, including RoseTTAFold and ESMFold, employ specialized neural network architectures driven by attention mechanisms to infer relationships between sequence and structure. At a fundamental level, these AI/ML models operate on the long-standing hypothesis that the structure of a protein is determined by its amino acid sequence. More recently, AlphaFold2 has been adapted for the prediction of multiple protein conformations by subsampling multiple sequence alignments. Herein, we provide an overview of the deterministic relationship between sequence and structure, which was hypothesized over half a century ago with profound implications for the biological sciences ever since. We postulate that protein conformational dynamics are also determined, at least in part, by amino acid sequence and that this relationship may be leveraged for construction of AI/ML models dedicated to predicting protein conformational ensembles. Accordingly, we describe a conceptual model architecture, which may be trained on sequence data in combination with conformationally sensitive structural information, coming primarily from nuclear magnetic resonance (NMR) spectroscopy. Notwithstanding certain limitations in this context, NMR offers abundant structural heterogeneity conducive to conformational ensemble prediction. As NMR and other data continue to accumulate, sequence-informed prediction of protein structural dynamics with AI/ML has the potential to emerge as a transformative capability across the biological sciences.

Artificial intelligence↗